Question: Aligning miRNA sequences
gravatar for Bioaln
4.1 years ago by
Bioaln340 wrote:
Hello. I've been recently dealing with miRNA sequences and aligning them has been somewhat problem to me. I've tried all major alignment software and results seem to be quite different for each aligner. Is there any recommended software for miRNA alignments? Muscle seems the most promising when analysing the results, yet I am not quite sure how to compare various alignment outputs. Thanks for any help.
mirna alignment • 2.1k views
ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 4.1 years ago by Bioaln340

Are trying to do multiple sequence alignment of the miRNAs (what MUSCLE does) or did you do small-RNAseq and now need to align that data or something else entirely?

ADD REPLYlink written 4.1 years ago by Devon Ryan94k
I am doing multiple sequence alignment, yes.
ADD REPLYlink written 4.1 years ago by Bioaln340

Here are the EBI MSA web services:

I am not aware of which one is most suitable for miRNA multiple alignment, but you could make a little benchmark dataset and then compare the alignments generated. However, I see the difficulties you are facing to compare and rate the alignments.

ADD REPLYlink written 4.1 years ago by Michael Dondrup47k
Thanks for the info. I used 5 of those tools and I will try to compare them in a statistical manner. What do you mean by benchmark dataset? Is it supposed to reveal differences amongst aligners, if so, thanks again for this info.
ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Bioaln340
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